ASCC1 Structures and Bioinformatics Reveal a Novel Helix-Clasp-Helix RNA-Binding Motif Linked to a Two-Histidine Phosphodiesterase

Authors

Naga Babu Chinnam
Roopa Thapar
Andrew S Arvai
Altaf H Sarker
Jennifer M Soll
Tanmoy Paul
Aleem Syed
Daniel J Rosenberg
Michal Hammel
Albino Bacolla
Panagiotis Katsonis
Abhishek Asthana
Miaw-Sheue Tsai
Ivaylo Ivanov
Olivier Lichtarge
Robert H Silverman
Nima Mosammaparast
Susan E Tsutakawa
John A Tainer

Publication Date

6-1-2024

Journal

Journal of Biological Chemistry

Abstract

Activating signal co-integrator complex 1 (ASCC1) acts with ASCC-ALKBH3 complex in alkylation damage responses. ASCC1 uniquely combines two evolutionarily ancient domains: nucleotide-binding K-Homology (KH) (associated with regulating splicing, transcriptional, and translation) and two-histidine phosphodiesterase (PDE; associated with hydrolysis of cyclic nucleotide phosphate bonds). Germline mutations link loss of ASCC1 function to spinal muscular atrophy with congenital bone fractures 2 (SMABF2). Herein analysis of The Cancer Genome Atlas (TCGA) suggests ASCC1 RNA overexpression in certain tumors correlates with poor survival, Signatures 29 and 3 mutations, and genetic instability markers. We determined crystal structures of Alvinella pompejana (Ap) ASCC1 and Human (Hs) PDE domain revealing high-resolution details and features conserved over 500 million years of evolution. Extending our understanding of the KH domain Gly-X-X-Gly sequence motif, we define a novel structural Helix-Clasp-Helix (HCH) nucleotide binding motif and show ASCC1 sequence-specific binding to CGCG-containing RNA. The V-shaped PDE nucleotide binding channel has two His-Φ-Ser/Thr-Φ (HXT) motifs (Φ being hydrophobic) positioned to initiate cyclic phosphate bond hydrolysis. A conserved atypical active-site histidine torsion angle implies a novel PDE substrate. Flexible active site loop and arginine-rich domain linker appear regulatory. Small-angle X-ray scattering (SAXS) revealed aligned KH-PDE RNA binding sites with limited flexibility in solution. Quantitative evolutionary bioinformatic analyses of disease and cancer-associated mutations support implied functional roles for RNA binding, phosphodiesterase activity, and regulation. Collective results inform ASCC1's roles in transactivation and alkylation damage responses, its targeting by structure-based inhibitors, and how ASCC1 mutations may impact inherited disease and cancer.

Keywords

Humans, Computational Biology, Crystallography, X-Ray, Phosphoric Diester Hydrolases, RNA-Binding Motifs

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Associated Data

PMID: 38750793