8WZC

NYN domain of human KHNYN complex with RNA

8WZC の概要

• エントリーDOI: 10.2210/pdb8wzc/pdb
• 分子名称: Protein KHNYN, RNA (5'-R(P*UP*UP*UP*AP*U)-3'), GLYCEROL, ... (5 entities in total)
• 機能のキーワード: khnyn, endonuclease, regnase, regulation, homeostasis, rna binding, rnase, hydrolase, hydrolase-rna complex, hydrolase/rna
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 20564.17

構造登録者

Hong, S.,Choe, J. (登録日: 2023-11-01, 公開日: 2024-09-11)

主引用文献

Hong, S.,Choe, J.
Crystal structure of NYN domain of Human KHNYN in complex with single strand RNA.
Biochem.Biophys.Res.Commun., 738:150545-150545, 2024

PubMed Abstract: KHNYN protein with a KH-like domain and a NYN endoribonuclease domain interacts with Zinc-finger antiviral protein (ZAP). ZAP isoforms recognize viral or cellular RNAs and recruit KHNYN to form the ZAP: KHNYN complex. Although the structures of several PIN/NYN domains have been determined, the precise substrate RNA binding mode remains poorly understood. This study presents the crystal structure of a complex of the NYN domain of KHNYN and a 7mer RNA from interferon lambda3 (IFNL3). Our structural analysis reveals that NYN domain of human KHNYN shares structural similarities with other NYN domains of ZC3H12àC proteins. The RNA is bound in the central groove region of the protein, facilitated by interactions including coordination by two Mg ions, hydrophobic interactions, and hydrogen bonds. In the observed RNA-protein complex, the U, A, and U bases are stacked on top of one another, while U and U bases adopt an "open" conformation (as opposed to base-stacked), forming a U-shaped overall structure. Mutagenesis studies underscore the significance of residues involved in RNA binding for RNase activity. Interestingly, NYN domain of human KHNYN forms a head-to-tail dimer in the crystal, a structural feature also observed in other homologous PIN/NYN proteins, with a residue from the symmetry mate contributing to hydrophobic interactions with the bound RNA.

PubMed: 39167961
DOI: 10.1016/j.bbrc.2024.150545

実験手法

X-RAY DIFFRACTION (1.925 Å)