PDBsum entry 2n3f

RNA binding protein

PDB id: 2n3f

Contents

Protein chain

153 a.a.

PDB id:

2n3f

Name:

RNA binding protein

Title:

Solution structure of both dsrbds of drb4 along with linker (viz. Drb4(1-153))

Structure:

Double-stranded RNA-binding protein 4. Chain: a. Fragment: drbm domains 1 and 2, residues 1-153. Synonym: dsrna-binding protein 4, atdrb4. Engineered: yes

Source:

Arabidopsis thaliana. Mouse-ear cress,thale-cress. Organism_taxid: 3702. Gene: dbr4, at3g62800, f26k9.230. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

10 models

Authors:

M.Deshmukh,S.Chiliveri

Key ref:

S.C.Chiliveri et al. (2017). DRB4 dsRBD1 drives dsRNA recognition in Arabidopsis thaliana tasi/siRNA pathway. Nucleic Acids Res, 45, 8551-8563. PubMed id: 28575480

Date:

29-May-15 Release date: 07-Sep-16

Protein chain

Q8H1D4  (DRB4_ARATH) -  Double-stranded RNA-binding protein 4 from Arabidopsis thaliana

Seq: 355 a.a.

Struc: 153 a.a.

Enzyme reactions

• Enzyme class: E.C.?

Nucleic Acids Res 45:8551-8563 (2017)

PubMed id: 28575480

DRB4 dsRBD1 drives dsRNA recognition in Arabidopsis thaliana tasi/siRNA pathway.

S.C.Chiliveri, R.Aute, U.Rai, M.V.Deshmukh.

ABSTRACT

In Arabidopsis thaliana, endogenous trans-acting and exogenous siRNA pathways are initiated by the interaction of DRB4 with trigger dsRNA. Further, DCL4:DRB4 complex cleaves the dsRNA into 21 bp siRNA. Understanding molecular determinants and mechanistic details of dsRNA recognition by DRB4 is vital for inducing long-term RNAi-mediated gene regulation in plants. Here, we present solution structures of individual and concatenated DRB4 dsRBDs and demonstrate modes of dsRNA binding by employing NMR, ITC and site-specific mutagenesis. While both dsRBDs adopt the canonical α-β-β-β-α fold, key structural differences and ms-μs dynamics located at the RNA binding region were observed for dsRBD1. These features favor dsRBD1 to orient itself and make stronger tripartite contact with dsRNA, a feature missing in dsRBD2. Additionally, the inter-domain orientation induced by the linker restricts the mobility of dsRBD2, resulting in the steric hindrance of α1 helix in dsRBD2, and leads in further reduction of its dsRNA binding activity. Our study deciphers functional roles of DRB4 domains by showing that dsRBD1 drives the tasiRNA/siRNA pathway. Furthermore, we identify a potential role of the C-terminal region of DRB4 in protein:protein interaction as it possesses six PxxP motifs, binds to Zn2+ and contains a small structural domain.