8WZC

NYN domain of human KHNYN complex with RNA

Summary for 8WZC

• Entry DOI: 10.2210/pdb8wzc/pdb
• Descriptor: Protein KHNYN, RNA (5'-R(P*UP*UP*UP*AP*U)-3'), GLYCEROL, ... (5 entities in total)
• Functional Keywords: khnyn, endonuclease, regnase, regulation, homeostasis, rna binding, rnase, hydrolase, hydrolase-rna complex, hydrolase/rna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 20564.17

Authors

Hong, S.,Choe, J. (deposition date: 2023-11-01, release date: 2024-09-11)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.925 Å)