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bioRxiv · 10.1101/2020.03.05.978023

Human DND1-RRM2 forms a non-canonical domain-swapped dimer

Kumari, P.·Bhavesh, N. S.
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Abstract

Human DND1 (Dead end protein homolog1) is an RNA binding protein. DND1 plays pivotal role in animal development and has been implicated in cancer. DND1 consists of two RNA recognition motifs (RRMs) in tandem and a double stranded RNA binding domain at the C terminal separated by 40 residues flexible linker. The conserved RNP site in the RRM1 domain helps in specific RNA recognition while the RNP sites in RRM2 are not well conserved. DND1 has been reported to be involved in inhibition of microRNA access to target mRNA and it also associate with CCR4-NOT complex that targets mRNA. In order to understand this intriguing contrasting molecular function, we have determined the 2.3 [A] resolution crystal structure of the human DND1 RRM2 domain. The structure revealed an interesting non-canonical RRM fold that is maintained by the formation of a domain swapped dimer between {beta}1 and {beta}4 strands across two chains. The domain swapping is attributed by a hinge loop between 2 and {beta}4 that helps in mediating a domain swap forming anti-parallel {beta} sheets. We have delineated the structural basis of stable dimer formation using the residue level dynamics of protein explored by NMR spectroscopy and MD simulations. Our structural and dynamics studies demonstrate the molecular basis for the dimerization of the RRM2 domain and shed light on the possibility for this motif for interaction with other proteins which helps in transcription regulation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/978023v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@4975d2org.highwire.dtl.DTLVardef@d65418org.highwire.dtl.DTLVardef@12b0272org.highwire.dtl.DTLVardef@ada8b7_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIFirst report of a domain swapped dimer formation by an RRM identified through crystal structure determination of the human DND1 RRM2 domain. C_LIO_LIRRM2 exhibit domain swapped dimerization attributed by hinge loop and disulfide bond formation. C_LIO_LIDimer formation is under redox regulation. C_LIO_LIMajor determinants of swapping were identified. C_LIO_LIDND1 RRM2 is not involved in RNA recognition. C_LI

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Kumari, P., Bhavesh, N. S.. 2020-03-05. Human DND1-RRM2 forms a non-canonical domain-swapped dimer. https://doi.org/10.1101/2020.03.05.978023

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