9E70

Human XRN1 with Adenosine-3',5'-Bisphosphate (pAp) Bound

Summary for 9E70

• Entry DOI: 10.2210/pdb9e70/pdb
• Descriptor: 5'-3' exoribonuclease 1, ADENOSINE-3'-5'-DIPHOSPHATE, MAGNESIUM ION, ... (7 entities in total)
• Functional Keywords: exonuclease, xrn1, pap, inhibitor, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 157813.77

Authors

Lockbaum, G.J.,Lynes, M.M.,Sickmier, E.A.,Grigoriu, S.,Boriack-Sjodin, P.A. (deposition date: 2024-10-31, release date: 2025-04-09, Last modification date: 2025-04-23)

Primary citation

Lockbaum, G.J.,Lynes, M.M.,Shen, S.A.,Liu, J.,Holt, N.,Nayak, S.P.,Knockenhauer, K.E.,Yao, S.,Sickmier, E.A.,Raman, A.,Wu, J.,Case, A.,Shehaj, L.,Buker, S.M.,Grigoriu, S.,Ribich, S.,Blakemore, S.J.,Sparling, B.A.,Duncan, K.W.,Copeland, R.A.,Silver, S.J.,Boriack-Sjodin, P.A.
Characterization of exoribonuclease XRN1 as a cancer target and identification of adenosine-3',5'-bisphosphate as a potent enzyme inhibitor.
Commun Biol, 8:589-589, 2025

PubMed Abstract: XRN1 (5'-3' exoribonuclease 1) degrades RNA from the 5' → 3' direction and utilizes both single- and double-stranded RNA as substrates. XRN1 plays a critical role in mRNA turnover as well as regulating the cellular response to viral infection. XRN1 also protects the cell by preventing endogenous double-stranded RNA accumulation. XRN1 was identified as a putative vulnerability in a subset of cancer cell lines through analysis of publicly available CRISPR data. The role of XRN1 was explored using a set of non-small cell lung cancer cell lines with differential predicted XRN1 dependency to validate XRN1 as an oncology target. In predicted sensitive cell lines, XRN1 knockout reduced proliferation, increased apoptosis and activated the pPKR and MDA5 dsRNA sensing pathways. To facilitate drug discovery targeting XRN1, a suite of biochemical and biophysical assays was developed. These assays were used to characterize adenosine-3',5'-bisphosphate (pAp), a non-selective nuclease inhibitor, as a nanomolar inhibitor of XRN1. Additionally, the crystal structure of human XRN1 was solved with pAp bound, demonstrating distinct interactions for the compound in the XRN1 active site. These studies provide a strong foundation for the discovery of potent, selective inhibitors of XRN1 as a novel approach to cancer therapeutics.

PubMed: 40205031
DOI: 10.1038/s42003-025-08005-y

Experimental method

X-RAY DIFFRACTION (2.1 Å)