9HTS

Human KHNYN KH domain

Summary for 9HTS

• Entry DOI: 10.2210/pdb9hts/pdb
• Descriptor: Protein KHNYN (2 entities in total)
• Functional Keywords: zap associated protein, antiviral protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 42241.69

Authors

Youle, R.L.,Cottee, M.A.,Taylor, I.A.,Morris, E.R. (deposition date: 2024-12-19, release date: 2025-02-26, Last modification date: 2025-08-06)

Primary citation

Youle, R.L.,Lista, M.J.,Bouton, C.,Kunzelmann, S.,Wilson, H.,Cottee, M.A.,Purkiss, A.G.,Morris, E.R.,Neil, S.J.D.,Taylor, I.A.,Swanson, C.M.
Structural and functional characterization of the extended-diKH domain from the antiviral endoribonuclease KHNYN.
J.Biol.Chem., 301:108336-108336, 2025

PubMed Abstract: Zinc finger antiviral protein (ZAP) binds CpG dinucleotides in viral RNA and targets them for decay. ZAP interacts with several cofactors to form the ZAP antiviral system, including KHNYN, a multidomain endoribonuclease required for ZAP-mediated RNA decay. However, it is unclear how the individual domains in KHNYN contribute to its activity. Here, we demonstrate that the KHNYN amino-terminal extended-diKH (ex-diKH) domain is required for antiviral activity and present its crystal structure. The structure belongs to a rare group of KH-containing domains, characterized by a noncanonical arrangement between two type 1 KH modules, with an additional helical bundle. N4BP1 is a KHNYN paralog with an ex-diKH domain that functionally complements the KHNYN ex-diKH domain. Interestingly, the ex-diKH domain structure is present in N4BP1-like proteins in lancelets, which are basal chordates, indicating that it is evolutionarily ancient. While many KH domains demonstrate RNA binding activity, biolayer interferometry and electrophoretic mobility shift assays indicate that the KHNYN ex-diKH domain does not bind RNA. Furthermore, residues required for canonical KH domains to bind RNA are not required for KHNYN antiviral activity. By contrast, an inter-KH domain cleft in KHNYN is a potential protein-protein interaction site, and mutations that eliminate arginine salt bridges at the edge of this cleft decrease KHNYN antiviral activity. This suggests that this domain could be a binding site for an unknown KHNYN cofactor.

PubMed: 39984050
DOI: 10.1016/j.jbc.2025.108336

Experimental method

X-RAY DIFFRACTION (2.198 Å)