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	How ATP and dATP reposition class III ribonucleotide reductase cone domains to regulate enzyme activity.
Journal, issue, pages	Sci Adv, Vol. 11, Issue 48, Page eady9156, Year 2025
Publish date	Nov 28, 2025
Authors	Gisele A Andree / Kelsey R Miller-Brown / Zhuangyu Zhao / Ally K Smith / Christopher D Dawson / Daniel J Deredge / Catherine L Drennan /
PubMed Abstract	Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides. In the majority of cases, RNR activity is allosterically regulated by the cellular 2'- ...Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides. In the majority of cases, RNR activity is allosterically regulated by the cellular 2'-deoxyadenosine 5'-triphosphate (dATP)/adenosine 5'-triphosphate (ATP) ratio. To investigate allosteric activity regulation in anaerobic or class III (glycyl radical containing) RNRs, we determine cryo-electron microscopy structures of the class III RNR from (StNrdD). We find that StNrdD's regulatory "cone" domains adopt markedly different conformations depending on whether the activator ATP or the inhibitor dATP is bound and that these different conformations alternatively position an "active site flap" toward the active site (ATP-bound) or away (dATP-bound). In contrast, the position of the glycyl radical domain is unaffected by the cone domain conformations, suggesting that StNrdD activity is regulated through control of substrate binding rather than control of radical transfer. Hydrogen-deuterium exchange mass spectrometry and mutagenesis support the structural findings. In addition, our structural data provide insight into the molecular basis by which ATP and dATP binding lead to the observed differential cone domain conformations.
External links	Sci Adv / PubMed:41313771 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.6 - 4.5 Å
Structure data	EMDB-46692: S. thermophilus class III ribonucleotide reductase signal subtracted cone domains and core Method: EM (single particle) / Resolution: 3.7 Å EMDB-46693: S. thermophilus class III ribonucleotide reductase focused refined core Method: EM (single particle) / Resolution: 3.1 Å EMDB-46696: S. thermophilus class III ribonucleotide reductase consensus Method: EM (single particle) / Resolution: 3.6 Å 46698 9dau EMDB-46698, PDB-9dau: S. thermophilus class III ribonucleotide reductase with dATP and TTP Method: EM (single particle) / Resolution: 3.6 Å EMDB-46712: S. thermophilus class III ribonucleotide reductase signal subtracted cone domains and core Method: EM (single particle) / Resolution: 4.1 Å EMDB-46713: S. thermophilus class III ribonucleotide reductase focused refined core Method: EM (single particle) / Resolution: 3.8 Å EMDB-46746: S. thermophilus class III ribonucleotide reductase consensus Method: EM (single particle) / Resolution: 4.5 Å 46747 9dca EMDB-46747, PDB-9dca: S. thermophilus class III ribonucleotide reductase with ATP and TTP Method: EM (single particle) / Resolution: 3.6 Å PDB-9d3x: Crystal structure of S. thermophilus class III ribonucleotide reductase bound to dATP Method: X-RAY DIFFRACTION / Resolution: 2.6 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ChemComp-ZN: Unknown entry ChemComp-SO4: SULFATE ION ChemComp-HOH: WATER ChemComp-TTP: THYMIDINE-5'-TRIPHOSPHATE ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM
Source	streptococcus thermophilus (bacteria)
Keywords	OXIDOREDUCTASE / Ribonucleotide reductase / allosteric regulation / cone domain / glycyl radical enzyme