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	Structural and mechanistic insights into a mesophilic prokaryotic Argonaute.
Journal, issue, pages	Nucleic Acids Res, Vol. 52, Issue 19, Page 11895-11910, Year 2024
Publish date	Oct 28, 2024
Authors	Xin Tao / Hui Ding / Shaowen Wu / Fei Wang / Hu Xu / Jie Li / Chao Zhai / Shunshun Li / Kai Chen / Shan Wu / Yang Liu / Lixin Ma /
PubMed Abstract	Argonaute (Ago) proteins are programmable nucleases found in all domains of life, playing a crucial role in biological processes like DNA/RNA interference and gene regulation. Mesophilic prokaryotic ...Argonaute (Ago) proteins are programmable nucleases found in all domains of life, playing a crucial role in biological processes like DNA/RNA interference and gene regulation. Mesophilic prokaryotic Agos (pAgos) have gained increasing research interest due to their broad range of potential applications, yet their molecular mechanisms remain poorly understood. Here, we present seven cryo-electron microscopy structures of Kurthia massiliensis Ago (KmAgo) in various states. These structures encompass the steps of apo-form, guide binding, target recognition, cleavage, and release, revealing that KmAgo employs a unique DDD catalytic triad, instead of a DEDD tetrad, for DNA target cleavage under 5'P-DNA guide conditions. Notably, the last catalytic residue, D713, is positioned outside the catalytic pocket in the absence of guide. After guide binding, D713 enters the catalytic pocket. In contrast, the corresponding catalytic residue in other Agos has been consistently located in the catalytic pocket. Moreover, we identified several sites exhibiting enhanced catalytic activity through alanine mutagenesis. These sites have the potential to serve as engineering targets for augmenting the catalytic efficiency of KmAgo. This structural analysis of KmAgo advances the understanding of the diversity of molecular mechanisms by Agos, offering insights for developing and optimizing mesophilic pAgos-based programmable DNA and RNA manipulation tools.
External links	Nucleic Acids Res / PubMed:39315697 / PubMed Central
Methods	EM (single particle)
Resolution	2.76 - 2.96 Å
Structure data	38355 8xhv EMDB-38355, PDB-8xhv: Structure of the Argonaute protein from Kurthia massiliensis in complex with guide DNA Method: EM (single particle) / Resolution: 2.81 Å 38408 8xjw EMDB-38408, PDB-8xjw: Structure of the Argonaute protein from Kurthia massiliensis in complex with guide DNA and 19-mer target RNA Method: EM (single particle) / Resolution: 2.84 Å 38409 8xjx EMDB-38409, PDB-8xjx: Structure of the Argonaute protein from Kurthia massiliensis in complex with guide DNA and 19-mer target DNA Method: EM (single particle) / Resolution: 2.78 Å 38412 8xk0 EMDB-38412, PDB-8xk0: Structure of the Argonaute protein from Kurthia massiliensis in complex with guide DNA and 19-mer target DNA in pre-cleavage state Method: EM (single particle) / Resolution: 2.96 Å 38414 8xk3 EMDB-38414, PDB-8xk3: Structure of the Argonaute protein from Kurthia massiliensis in complex with guide DNA and 19-mer target DNA in target-cleaved state Method: EM (single particle) / Resolution: 2.76 Å 38415 8xk4 EMDB-38415, PDB-8xk4: Structure of the Argonaute protein from Kurthia massiliensis in complex with guide DNA and 19-mer target DNA in target-released state Method: EM (single particle) / Resolution: 2.94 Å
Chemicals	ChemComp-MN: Unknown entry ChemComp-HOH: WATER ChemComp-DC: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / dCMP*YM
Source	kurthia massiliensis (bacteria)
Keywords	DNA BINDING PROTEIN/DNA / Mesophilic prokaryotic Argonaute / DNA BINDING PROTEIN-DNA COMPLEX / DNA BINDING PROTEIN