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	Autoinhibition of a clamp-loader ATPase revealed by deep mutagenesis and cryo-EM.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 31, Issue 3, Page 424-435, Year 2024
Publish date	Jan 4, 2024
Authors	Kendra Marcus / Yongjian Huang / Subu Subramanian / Christine L Gee / Kent Gorday / Sam Ghaffari-Kashani / Xiao Ran Luo / Lisa Zheng / Michael O'Donnell / Sriram Subramaniam / John Kuriyan /
PubMed Abstract	Clamp loaders are AAA+ ATPases that facilitate high-speed DNA replication. In eukaryotic and bacteriophage clamp loaders, ATP hydrolysis requires interactions between aspartate residues in one ...Clamp loaders are AAA+ ATPases that facilitate high-speed DNA replication. In eukaryotic and bacteriophage clamp loaders, ATP hydrolysis requires interactions between aspartate residues in one protomer, present in conserved 'DEAD-box' motifs, and arginine residues in adjacent protomers. We show that functional defects resulting from a DEAD-box mutation in the T4 bacteriophage clamp loader can be compensated by widely distributed single mutations in the ATPase domain. Using cryo-EM, we discovered an unsuspected inactive conformation of the clamp loader, in which DNA binding is blocked and the catalytic sites are disassembled. Mutations that restore function map to regions of conformational change upon activation, suggesting that these mutations may increase DNA affinity by altering the energetic balance between inactive and active states. Our results show that there are extensive opportunities for evolution to improve catalytic efficiency when an inactive intermediate is involved.
External links	Nat Struct Mol Biol / PubMed:38177685 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.628 - 3.21 Å
Structure data	42399 8unf EMDB-42399, PDB-8unf: Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and DNA Method: EM (single particle) / Resolution: 3.15 Å 42402 8unh EMDB-42402, PDB-8unh: Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp Method: EM (single particle) / Resolution: 3.21 Å PDB-8uh7: Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Method: X-RAY DIFFRACTION / Resolution: 2.628 Å PDB-8uk9: Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog Method: X-RAY DIFFRACTION / Resolution: 3.1 Å
Chemicals	ChemComp-08T: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ChemComp-MG: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM / Adenosine diphosphate ChemComp-HOH: WATER / Water ChemComp-AF3: ALUMINUM FLUORIDE / Aluminium fluoride ChemComp-AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogueYM
Source	tequatrovirus t4 tequatrovirus
Keywords	REPLICATION/DNA / Clamp loader / T4 / AAA+ATPase / REPLICATION / REPLICATION-DNA complex / DNA BINDING PROTEIN/DNA / DNA Replication / AAA+ ATPase / Bacteriophage / Complex / DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex / active / DNA-bound / autoinhibited / DNA-free / catalytically inactive / stable