title: Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.
abstract: We report on crystal structures of ternary Thermus thermophilus Argonaute (TtAgo) complexes with 5'-phosphorylated guide DNA and a series of DNA targets. These ternary complex structures of cleavage-incompatible, cleavage-compatible, and postcleavage states solved at improved resolution up to 2.2 Å have provided molecular insights into the orchestrated positioning of catalytic residues, a pair of Mg(2+) cations, and the putative water nucleophile positioned for in-line attack on the cleavable phosphate for TtAgo-mediated target cleavage by a RNase H-type mechanism. In addition, these ternary complex structures have provided insights into protein and DNA conformational changes that facilitate transition between cleavage-incompatible and cleavage-compatible states, including the role of a Glu finger in generating a cleavage-competent catalytic Asp-Glu-Asp-Asp tetrad. Following cleavage, the seed segment forms a stable duplex with the complementary segment of the target strand.
authors.affiliation: Laboratory of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Gang
authors.initials: G
authors.lastname: Sheng
authors.forename: Hongtu
authors.initials: H
authors.lastname: Zhao
authors.forename: Jiuyu
authors.initials: J
authors.lastname: Wang
authors.forename: Yu
authors.initials: Y
authors.lastname: Rao
authors.forename: Wenwen
authors.initials: W
authors.lastname: Tian
authors.forename: Daan C
authors.initials: DC
authors.lastname: Swarts
authors.forename: John
authors.initials: J
authors.lastname: van der Oost
authors.forename: Dinshaw J
authors.initials: DJ
authors.lastname: Patel
authors.forename: Yanli
authors.initials: Y
authors.lastname: Wang
mesh_terms: D060565:Argonaute Proteins / Q000737:chemistry* / Q000378:metabolism; D002384:Catalysis; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D011487:Protein Conformation; D016963:Thermus thermophilus / Q000737:chemistry* / Q000378:metabolism
chemical_list: D060565:Argonaute Proteins; D004269:DNA, Bacterial
keywords: DNA guide-DNA target; bacterial Argonaute; catalytic mechanism