ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase

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

doi:10.1016/j.jbc.2024.107368

ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase

J Biol Chem. 2024 May 14;300(6):107368. doi: 10.1016/j.jbc.2024.107368. Online ahead of print.

Authors

Naga Babu Chinnam¹, Roopa Thapar¹, Andrew S Arvai², Altaf H Sarker³, Jennifer M Soll⁴, Tanmoy Paul⁵, Aleem Syed¹, Daniel J Rosenberg⁶, Michal Hammel⁶, Albino Bacolla¹, Panagiotis Katsonis⁷, Abhishek Asthana⁸, Miaw-Sheue Tsai³, Ivaylo Ivanov⁵, Olivier Lichtarge⁷, Robert H Silverman⁸, Nima Mosammaparast⁴, Susan E Tsutakawa⁹, John A Tainer¹⁰

Affiliations

¹ Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
² Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
³ Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
⁴ Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, USA.
⁵ Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA.
⁶ Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
⁷ Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
⁸ Department Cancer Biology, Cleveland Clinic Foundation, Lerner Research Institute, Cleveland, Ohio, USA.
⁹ Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA. Electronic address: setsutakawa@lbl.gov.
¹⁰ Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA; Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA. Electronic address: JTainer@mdanderson.org.

PMID: 38750793
DOI: 10.1016/j.jbc.2024.107368

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: DNA repair; RNA; binding protein; conformational change; crystallography; genomics; inhibition mechanism; phosphodiesterase: cancer; small angle X-ray scattering (SAXS); structural biology.

Abstract

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