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	Pretransition state and apo structures of the filament-forming enzyme SgrAI elucidate mechanisms of activation and substrate specificity.
Journal, issue, pages	J Biol Chem, Vol. 298, Issue 4, Page 101760, Year 2022
Publish date	Feb 21, 2022
Authors	Zelin Shan / Niloofar Ghadirian / Dmitry Lyumkis / Nancy C Horton /
PubMed Abstract	Enzyme filamentation is a widespread phenomenon that mediates enzyme regulation and function. For the filament-forming sequence-specific DNA endonuclease SgrAI, the process of filamentation both ...Enzyme filamentation is a widespread phenomenon that mediates enzyme regulation and function. For the filament-forming sequence-specific DNA endonuclease SgrAI, the process of filamentation both accelerates its DNA cleavage activity and expands its DNA sequence specificity, thus allowing for many additional DNA sequences to be rapidly cleaved. Both outcomes-the acceleration of DNA cleavage and the expansion of sequence specificity-are proposed to regulate critical processes in bacterial innate immunity. However, the mechanistic bases underlying these events remain unclear. Herein, we describe two new structures of the SgrAI enzyme that shed light on its catalytic function. First, we present the cryo-EM structure of filamentous SgrAI bound to intact primary site DNA and Ca resolved to ∼2.5 Å within the catalytic center, which represents the trapped enzyme-DNA complex prior to the DNA cleavage reaction. This structure reveals important conformational changes that contribute to the catalytic mechanism and the binding of a second divalent cation in the enzyme active site, which is expected to contribute to increased DNA cleavage activity of SgrAI in the filamentous state. Second, we present an X-ray crystal structure of DNA-free (apo) SgrAI resolved to 2.0 Å resolution, which reveals a disordered loop involved in DNA recognition. Collectively, these multiple new observations clarify the mechanism of expansion of DNA sequence specificity of SgrAI, including the indirect readout of sequence-dependent DNA structure, changes in protein-DNA interactions, and the disorder-to-order transition of a crucial DNA recognition element.
External links	J Biol Chem / PubMed:35202658 / PubMed Central
Methods	EM (helical sym.) / X-ray diffraction
Resolution	2.02 - 2.7 Å
Structure data	25404 7ss5 EMDB-25404: Activated filamentous SgrAI endonuclease with Ca2+ and intact primary site DNA PDB-7ss5: Activated SgrAI endonuclease DNA-bound dimer with Ca2+ and intact primary site DNA Method: EM (helical sym.) / Resolution: 2.7 Å PDB-7s8d: Structure of DNA-free SgrAI Method: X-RAY DIFFRACTION / Resolution: 2.02 Å
Chemicals	ChemComp-CA: Unknown entry ChemComp-HOH: WATER
Source	streptomyces griseus (bacteria)
Keywords	DNA BINDING PROTEIN / type II restriction endonuclease / nuclease / DNA cleavage / anti-viral / bacterial innate immunity / filament forming / HYDROLASE/DNA / restriction endonuclease / DNAse / allostery / filament / hyper-activation / substrate specificity / HYDROLASE-DNA complex