PDBsum entry 4kpy

DNA binding protein/DNA

PDB id: 4kpy

Contents

Protein chains

676 a.a.

DNA/RNA

Ligands

TMP ×2

Metals

_MN ×6

Waters ×356

References listed in PDB file

Key reference

• Title: Structure-Based cleavage mechanism of thermus thermophilus argonaute DNA guide strand-Mediated DNA target cleavage.
• Authors: G.Sheng, H.Zhao, J.Wang, Y.Rao, W.Tian, D.C.Swarts, J.Van der oost, D.J.Patel, Y.Wang.
• Ref.: Proc Natl Acad Sci U S A, 2014, 111, 652-657. [DOI no: 10.1073/pnas.1321032111]
• PubMed id: 24374628

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.