2LTR

Solution structure of RDE-4(32-136)

Summary for 2LTR

• Entry DOI: 10.2210/pdb2ltr/pdb
• Related: 2LTS
• NMR Information: BMRB: 17703
• Descriptor: Protein RDE-4 (1 entity in total)
• Functional Keywords: rde-4, dsrbd1, rnai, rde-4dc, rna binding protein
• Biological source: Caenorhabditis elegans (nematode)
• Total number of polymer chains: 1
• Total formula weight: 27860.63

Authors

Deshmukh, M.,Chiliveri, S. (deposition date: 2012-05-31, release date: 2013-12-04, Last modification date: 2024-05-15)

Primary citation

Chiliveri, S.C.,Deshmukh, M.V.
Structure of RDE-4 dsRBDs and mutational studies provide insights into dsRNA recognition in the Caenorhabditis elegans RNAi pathway.
Biochem.J., 458:119-130, 2014

PubMed Abstract: The association of RDE-4 (RNAi defective 4), a protein containing two dsRBDs (dsRNA-binding domains), with long dsRNA and Dcr-1 (Dicer1 homologue) initiates the siRNA pathway in Caenorhabditis elegans. Unlike its homologues in higher eukaryotes, RDE-4 dsRBDs possess weak (micromolar) affinity for short dsRNA. With increasing length of dsRNA, RDE-4 exhibits enhanced affinity due to co-operativity. The linker and dsRBD2 are indispensable for RDE-4's simultaneous interaction with dsRNA and Dcr-1. In the present study, we have determined the solution structures of RDE-4 constructs that contain both dsRBDs and the linker region. In addition to the canonical dsRBD fold, both dsRBDs of RDE-4 show modified structural features such as truncation in the β1-β2 loop that rationalize RDE-4's relatively weak dsRNA affinity. Structure and binding studies demonstrate that dsRBD2 plays a decisive role in the RDE-4-dsRNA interaction; however, in contrast with previous findings, we found ephemeral interaction of RDE-4 dsRBD1 with dsRNA. More importantly, mutations in two tandem lysine residues (Lys217 and Lys218) in dsRBD2 impair RDE-4's dsRNA-binding ability and could obliterate RNAi initiation in C. elegans. Additionally, we postulate a structural basis for the minimal requirement of linker and dsRBD2 for RDE-4's association with dsRNA and Dcr-1.

PubMed: 24256178
DOI: 10.1042/BJ20131347

Experimental method

SOLUTION NMR