Activity and structure of human (d)CTP deaminase CDADC1

• 成果类型: Article
• 署名作者: Slyvka, Anton; Rathore, Ishan; Yang, Renbin; Gewartowska, Olga; Kanai, Tapan; Lountos, George T.; Skowronek, Krzysztof; Czarnocki-Cieciura, Mariusz; Wlodawer, Alexander; Bochtler, Matthias
• 署名单位: Miedzynarodowy Instytut Biologii Molekularnej i Komorkowej; National Institutes of Health (NIH) - USA; NIH National Cancer Institute (NCI); National Institutes of Health (NIH) - USA; NIH National Cancer Institute (NCI); Frederick National Laboratory for Cancer Research; Miedzynarodowy Instytut Biologii Molekularnej i Komorkowej; National Institutes of Health (NIH) - USA; NIH National Cancer Institute (NCI); Frederick National Laboratory for Cancer Research; Miedzynarodowy Instytut Biologii Molekularnej i Komorkowej; Miedzynarodowy Instytut Biologii Molekularnej i Komorkowej; Polish Academy of Sciences; Institute of Biochemistry & Biophysics - Polish Academy of Sciences
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-9203
• DOI: 10.1073/pnas.2424245122
• 发表日期: 2025-05-13
• 关键词: dctp deaminase; deoxycytidylate deaminase; cytidine deaminase; crystal-structure; escherichia-coli; substrate; mechanism; nyd-sp15; dutpase; binding

摘要

Vertebrates have evolved an understudied protein termed CDADC1 (NYD-SP15) that contains an inactive N-terminal and active C-terminal DCTD-like domain. Here, we show that human CDADC1 is a (d)CTP-specific deaminase, with a roughly 2-fold in vitro preference for dCTP over CTP. We determined high-resolution cryo-EM structures of CDADC1 in the absence of substrate and in complex with dCTP and 5-methyl-dCTP. The structures show that CDADC1 forms trimers and dimers of trimers in solution. The (d)CTP substrate is selected by a narrow pocket for the cytosine base and multiple lysine and arginine contacts to the triphosphate. Substrate binding promotes the association of trimers into hexamers and the transition of the hexamers from a loose to a tighter arrangement. Genetic experiments in mice show that loss of Cdadc1 is surprisinglywell tolerated, even in the absence of the dCMP deaminase Dctd that is considered as the main source of dUMP, the precursor of dTTP.