3OMC

Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R4me2s

3OMC の概要

• エントリーDOI: 10.2210/pdb3omc/pdb
• 分子名称: Staphylococcal nuclease domain-containing protein 1, SYNTHETIC PEPTIDE, CHLORIDE ION, ... (4 entities in total)
• 機能のキーワード: staphylococcal nuclease domain-containing protein 1, tdrd11, snd1, piwil1/miwi, structural genomics consortium, sgc, p100 extended tudor domain, transcription regulation, symmetrically dimethylated arginine peptides derived from piwil1, transcription regulator
• 由来する生物種: Homo sapiens (Human); 詳細
• 細胞内の位置: Cytoplasm : Q7KZF4
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 61406.37

構造登録者

Lam, R.,Liu, K.,Guo, Y.H.,Bian, C.B.,Xu, C.,MacKenzie, F.,Bountra, C.,Weigelt, J.,Arrowsmith, C.H.,Edwards, A.M.,Bochkarev, A.,Min, J.,Structural Genomics Consortium (SGC) (登録日: 2010-08-26, 公開日: 2010-09-15, 最終更新日: 2024-11-20)

主引用文献

Liu, K.,Chen, C.,Guo, Y.,Lam, R.,Bian, C.,Xu, C.,Zhao, D.Y.,Jin, J.,MacKenzie, F.,Pawson, T.,Min, J.
Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain.
Proc.Natl.Acad.Sci.USA, 107:18398-18403, 2010

PubMed Abstract: Arginine methylation modulates diverse cellular processes and represents a molecular signature of germ-line-specific Piwi family proteins. A subset of Tudor domains recognize arginine methylation modifications, but the binding mechanism has been lacking. Here we establish that, like other germ-line Tudor proteins, the ancestral staphylococcal nuclease domain-containing 1 (SND1) polypeptide is expressed and associates with PIWIL1/Miwi in germ cells. We find that human SND1 binds PIWIL1 in an arginine methylation-dependent manner with a preference for symmetrically dimethylated arginine. The entire Tudor domain and a bifurcated SN domain are required for this binding activity, whereas the canonical Tudor domain alone is insufficient for methylarginine ligand binding. Crystal structures show that the intact SND1 extended Tudor domain forms a wide and negatively charged binding groove, which can accommodate distinct symmetrically dimethylated arginine peptides from PIWIL1 in different orientations. This analysis explains how SND1 preferentially recognizes symmetrical dimethylarginine via an aromatic cage and conserved hydrogen bonds, and provides a general paradigm for the binding mechanisms of methylarginine-containing peptides by extended Tudor domains.

PubMed: 20937909
DOI: 10.1073/pnas.1013106107

実験手法

X-RAY DIFFRACTION (1.77 Å)