PDBsum entry: 3fdr

RNA binding protein

PDB id: 3fdr

Contents

Protein chain

89 a.a. *

Waters ×84

* Residue conservation analysis

PDB id:

3fdr

Name:

RNA binding protein

Title:

Crystal structure of tdrd2

Structure:

Tudor and kh domain-containing protein. Chain: a. Fragment: tudor domain. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: tdrkh, tdrd2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.75Å R-factor: 0.216 R-free: 0.257

Authors:

M.F Amaya,M.A.Adams,Y.Guo,Y.Li,I.Kozieradzki,A.M.Edwards, C.H.Arrowsmith,J.Weigelt,C.Bountra,A.Bochkarev,J.Min, Structural Genomics Consortium (Sgc)

Key ref:

C.Chen et al. (2009). Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi. Proc Natl Acad Sci U S A, 106, 20336-20341. PubMed id: 19918066 DOI: 10.1073/pnas.0911640106

Date:

26-Nov-08 Release date: 06-Jan-09

Protein chain

Q9Y2W6  (TDRKH_HUMAN) -  Tudor and KH domain-containing protein

Seq: 561 a.a.

Struc: 89 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (1 term)

DOI no: 10.1073/pnas.0911640106

Proc Natl Acad Sci U S A 106:20336-20341 (2009)

PubMed id: 19918066

Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi.

C.Chen, J.Jin, D.A.James, M.A.Adams-Cioaba, J.G.Park, Y.Guo, E.Tenaglia, C.Xu, G.Gish, J.Min, T.Pawson.

ABSTRACT

Tudor domains are protein modules that mediate protein-protein interactions, potentially by binding to methylated ligands. A group of germline specific single and multiTudor domain containing proteins (TDRDs) represented by drosophila Tudor and its mammalian orthologs Tdrd1, Tdrd4/RNF17, and Tdrd6 play evolutionarily conserved roles in germinal granule/nuage formation and germ cell specification and differentiation. However, their physiological ligands, and the biochemical and structural basis for ligand recognition, are largely unclear. Here, by immunoprecipitation of endogenous murine Piwi proteins (Miwi and Mili) and proteomic analysis of complexes related to the piRNA pathway, we show that the TDRD group of Tudor proteins are physiological binding partners of Piwi family proteins. In addition, mass spectrometry indicates that arginine residues in RG repeats at the N-termini of Miwi and Mili are methylated in vivo. Notably, we found that Tdrkh/Tdrd2, a novel single Tudor domain containing protein identified in the Miwi complex, is expressed in the cytoplasm of male germ cells and directly associates with Miwi. Mutagenesis studies mapped the Miwi-Tdrkh interaction to the very N-terminal RG/RA repeats of Miwi and showed that the Tdrkh Tudor domain is critical for binding. Furthermore, we have solved the crystal structure of the Tdrkh Tudor domain, which revealed an aromatic binding pocket and negatively charged binding surface appropriate for accommodating methylated arginine. Our findings identify a methylation-directed protein interaction mechanism in germ cells mediated by germline Tudor domains and methylated Piwi family proteins, and suggest a complex mode of regulating the organization and function of Piwi proteins in piRNA silencing pathways.

Selected figure(s)

Figure 2.
Arginine methylation sites detected on endogenous Miwi and Mili by mass spectrometry. N-terminal RG/RA-rich sequences are show in red. Identified methylation sites (Me) are shown above the relevant arginine, with the residue numbers underneath.

Figure 5.
Crystal structure of the Tudor domain of Tdrkh. (A) Ribbon representation of the Tdrkh Tudor domain crystal structure. The residues comprising the aromatic binding pocket are shown in yellow. (B) Ribbon representation of the Snd1 Tudor domain crystal structure. (C) Surface representation of the Tdrkh Tudor domain crystal structure. (D) Surface representation of the Snd1 Tudor domain crystal structure. (E) Molecular docking of a GRG peptide with sDMA into the aromatic cage of the Tdrkh Tudor domain.

Figures were selected by an automated process.