Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Activity and structure of human (d)CTP deaminase CDADC1.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 122, Issue 19, Page e2424245122, Year 2025
Publish date	May 13, 2025
Authors	Anton Slyvka / Ishan Rathore / Renbin Yang / Olga Gewartowska / Tapan Kanai / George T Lountos / Krzysztof Skowronek / Mariusz Czarnocki-Cieciura / Alexander Wlodawer / Matthias Bochtler /
PubMed Abstract	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.
External links	Proc Natl Acad Sci U S A / PubMed:40324085 / PubMed Central
Methods	EM (single particle)
Resolution	2.8 - 3.7 Å
Structure data	52121 9hfq EMDB-52121, PDB-9hfq: Cryo-EM structure of human CDADC1 inactive mutant (E400A): trimer without a ligand Method: EM (single particle) / Resolution: 3.06 Å 52122 9hfr EMDB-52122, PDB-9hfr: Cryo-EM structure of human CDADC1 inactive mutant (E400A): hexamer without a ligand Method: EM (single particle) / Resolution: 3.7 Å EMDB-52123: Cryo-EM structure of human CDADC1 inactive mutant (E400A): trimer in the presence of dCTP in solution (not bound) Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 2.8 Å EMDB-52125: Cryo-EM structure of human CDADC1 inactive mutant (E400A): trimer in the presence of 5mdCTP in solution (not bound) Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 2.9 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-HOH: WATER ChemComp-DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE PDB Unreleased entry PDB-1i2i: CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM OMP SYNTHASE IN COMPLEX WITH MGPRPP AND OROTATE
Source	homo sapiens (human)
Keywords	HYDROLASE / Human dCTP deaminase / trimer / Zinc-dependent / Nucleotide metabolism