Slyvka Anton, Rathore Ishan, Yang Renbin, Gewartowska Olga, Kanai Tapan, Lountos George T, Skowronek Krzysztof, Czarnocki-Cieciura Mariusz, Wlodawer Alexander, Bochtler Matthias
Laboratory of Structural Biology, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland.
Center for Structural Biology, National Cancer Institute, NIH, Frederick, MD 21702.
Proc Natl Acad Sci U S A. 2025 May 13;122(19):e2424245122. doi: 10.1073/pnas.2424245122. Epub 2025 May 5.
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 surprisingly well tolerated, even in the absence of the dCMP deaminase Dctd that is considered as the main source of dUMP, the precursor of dTTP.
脊椎动物进化出了一种研究较少的蛋白质，称为CDADC1（NYD-SP15），它含有一个无活性的N端和一个有活性的C端DCTD样结构域。在这里，我们表明人类CDADC1是一种（d）CTP特异性脱氨酶，在体外对dCTP的偏好大约是CTP的2倍。我们确定了CDADC1在无底物状态下以及与dCTP和5-甲基-dCTP结合时的高分辨率冷冻电镜结构。这些结构表明，CDADC1在溶液中形成三聚体和三聚体二聚体。（d）CTP底物通过一个狭窄的胞嘧啶碱基口袋以及与三磷酸的多个赖氨酸和精氨酸接触来选择。底物结合促进三聚体缔合形成六聚体，并使六聚体从松散排列转变为紧密排列。小鼠的基因实验表明，即使在没有被认为是dTTP前体dUMP的主要来源的dCMP脱氨酶Dctd的情况下，Cdadc1的缺失也出人意料地具有良好的耐受性。
