EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Activity and structure of human (d)CTP deaminase CDADC1.
ジャーナル・号・ページ	Proc Natl Acad Sci U S A, Vol. 122, Issue 19, Page e2424245122, Year 2025
掲載日	2025年5月13日
著者	Anton Slyvka / Ishan Rathore / Renbin Yang / Olga Gewartowska / Tapan Kanai / George T Lountos / Krzysztof Skowronek / Mariusz Czarnocki-Cieciura / Alexander Wlodawer / Matthias Bochtler /
PubMed 要旨	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- ...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.
リンク	Proc Natl Acad Sci U S A / PubMed:40324085 / PubMed Central
手法	EM (単粒子)
解像度	2.8 - 3.7 Å
構造データ	52121 9hfq EMDB-52121, PDB-9hfq: Cryo-EM structure of human CDADC1 inactive mutant (E400A): trimer without a ligand 手法: EM (単粒子) / 解像度: 3.06 Å 52122 9hfr EMDB-52122, PDB-9hfr: Cryo-EM structure of human CDADC1 inactive mutant (E400A): hexamer without a ligand 手法: EM (単粒子) / 解像度: 3.7 Å EMDB-52123: Cryo-EM structure of human CDADC1 inactive mutant (E400A): trimer in the presence of dCTP in solution (not bound) 手法: EM (単粒子) / 解像度: 3.08 Å 52124 9hfs EMDB-52124, PDB-9hfs: Cryo-EM structure of human CDADC1 inactive mutant (E400A): hexamer with dCTP bound in the active site 手法: EM (単粒子) / 解像度: 2.8 Å EMDB-52125: Cryo-EM structure of human CDADC1 inactive mutant (E400A): trimer in the presence of 5mdCTP in solution (not bound) 手法: EM (単粒子) / 解像度: 2.81 Å 52126 9hft EMDB-52126, PDB-9hft: Cryo-EM structure of human CDADC1 inactive mutant (E400A): hexamer with 5mdCTP bound in the active site 手法: EM (単粒子) / 解像度: 2.9 Å
化合物	ChemComp-ZN: Unknown entry ChemComp-HOH: WATER ChemComp-DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / dCTP PDB 未公開エントリ PDB-1i2i: CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM OMP SYNTHASE IN COMPLEX WITH MGPRPP AND OROTATE
由来	homo sapiens (ヒト)
キーワード	HYDROLASE / Human dCTP deaminase / trimer / Zinc-dependent / Nucleotide metabolism