ZBP1 recognition of -actin zipcode induces RNA looping

Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
Genes & development (Impact Factor: 10.8). 01/2010; 24(2):148-58. DOI: 10.1101/gad.1862910
Source: PubMed


ZBP1 (zipcode-binding protein 1) was originally discovered as a trans-acting factor for the "zipcode" in the 3' untranslated region (UTR) of the beta-actin mRNA that is important for its localization and translational regulation. Subsequently, ZBP1 has been found to be a multifunctional regulator of RNA metabolism that controls aspects of localization, stability, and translation for many mRNAs. To reveal how ZBP1 recognizes its RNA targets, we biochemically characterized the interaction between ZBP1 and the beta-actin zipcode. The third and fourth KH (hnRNP K homology) domains of ZBP1 specifically recognize a bipartite RNA element located within the first 28 nucleotides of the zipcode. The spacing between the RNA sequences is consistent with the structure of IMP1 KH34, the human ortholog of ZBP1, that we solved by X-ray crystallography. The tandem KH domains are arranged in an intramolecular anti-parallel pseudodimer conformation with the canonical RNA-binding surfaces at opposite ends of the molecule. This orientation of the KH domains requires that the RNA backbone must undergo an approximately 180 degrees change in direction in order for both KH domains to contact the RNA simultaneously. The RNA looping induced by ZBP1 binding provides a mechanism for specific recognition and may facilitate the assembly of post-transcriptional regulatory complexes by remodeling the bound transcript.

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    • "Biochemical characterization of the ZBP1 recognition motif reveals that the ZBP1 KH34 region functions as a single unit to interact with the zipcode of b-actin mRNA (Chao et al., 2010). Knockdown of ZBP1 by small interfering (si)RNA impairs cellular adhesion, motility and invadopodia formation (Vikesaa et al., 2006; Gu et al., 2012; Katz et al., 2012). "
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    • "The coding region determinant-binding protein (CRD-BP), also commonly known as insulin-like growth factor II mRNA-binding protein 1 (IMP1), is a member of the conserved VICKZ family of RNA-binding proteins that are characterized by the presence of two N-terminal RNA-recognition motifs (RRMs) followed by four C-terminal KH [hnRNP (heterogenous nuclear ribonucleoprotein) K-homology] domains [1]–[4]. CRD-BP has about 95% protein sequence identity to the chicken zipcode-binding protein 1 (ZBP1) [2] that associates with β–actin mRNA [5], [6]. "
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