The Structure of the C-Terminal KH Domains of KSRP Reveals a Noncanonical Motif Important for mRNA Degradation

Abstract

The AU-rich element (ARE) RNA-binding protein KSRP (K-homology splicing regulator protein) contains four KH domains and promotes the degradation of specific mRNAs that encode proteins with functions in cellular proliferation and inflammatory response. The fourth KH domain (KH4) is essential for mRNA recognition and decay but requires the third KH domain (KH3) for its function. We show that KH3 and KH4 behave as independent binding modules and can interact with different regions of the AU-rich RNA targets of KSRP. This provides KSRP with the structural flexibility needed to recognize a set of different targets in the context of their 3'UTR structural settings. Surprisingly, we find that KH4 binds to its target AREs with lower affinity than KH3 and that KSRP's mRNA binding, and mRNA degradation activities are closely associated with a conserved structural element of KH4.

The human RBPome: From genes and proteins to human disease

“…The domain distribution of this catalogue ( Figure 1B) illustrates the presence of various known and well-studied RNA binding domains like RRM (RNA recognition motif) [30], K-homology (KH) [31,32], DEAD/DEAH box [33], dsrm [34], WD40 [35] in addition to unclassified domains like the Pkinase domain of EIF2AK2 that auto phosphorylates upon binding of RNA to the dsRBD domain of EIF2AK2 [36,37]. Also notable is the Calponin homology (CH) domain found in both cytoskeletal and signalling proteins [38].…”

The roles of S1 RNA-binding domains in Rrp5's interactions with pre-rRNA

“…While each one of the domains alone recognizes RNA with weak, although not identical, affinity, combining any two increases RNA-binding strength (Garcia-Mayoral et al 2007;Diaz-Moreno et al 2010). Furthermore, the increase is completely additive in the case of KH3 and KH4, which are linked by a flexible linker, while the increase appears subadditive in the case of KH2 and KH3 (Garcia-Mayoral et al 2007. Finally, disrupting the interaction between KH2/3 via a point mutation increases the RNA affinity, albeit weakly (Diaz-Moreno et al 2010).…”

“…For example, KSRP, a protein involved in splicing and degradation of specific target mRNAs, has four KH domains (Gherzi et al 2004). While each one of the domains alone recognizes RNA with weak, although not identical, affinity, combining any two increases RNA-binding strength (Garcia-Mayoral et al 2007;Diaz-Moreno et al 2010). Furthermore, the increase is completely additive in the case of KH3 and KH4, which are linked by a flexible linker, while the increase appears subadditive in the case of KH2 and KH3 (Garcia-Mayoral et al 2007.…”

KH–RNA interactions: back in the groove

“…Specific recognition of longer sequences by individual domains is achieved by expanding the classical KH fold with additional secondary structure elements that elongate the RNA recognition surface [17,18]. The best studied of these expanded KH folds is the Signal Transduction and Activation of RNA (STAR) fold, which mediates RNA recognition in a family of proteins important to splicing, mRNA shuttling and translational repression (Figure 3a) [8,19-21].…”