4KPY

DNA binding protein and DNA complex structure

Summary for 4KPY

• Entry DOI: 10.2210/pdb4kpy/pdb
• Descriptor: Uncharacterized protein, DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'), DNA (5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'), ... (7 entities in total)
• Functional Keywords: argonaute, rna interference, dna interference, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Thermus thermophilus; More
• Total number of polymer chains: 8
• Total formula weight: 178935.58

Authors

Sheng, G.,Zhao, H.,Wang, J.,Rao, Y.,Wang, Y. (deposition date: 2013-05-14, release date: 2014-01-29, Last modification date: 2024-05-29)

Primary citation

Sheng, G.,Zhao, H.,Wang, J.,Rao, Y.,Tian, W.,Swarts, D.C.,van der Oost, J.,Patel, D.J.,Wang, Y.
Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.
Proc.Natl.Acad.Sci.USA, 111:652-657, 2014

PubMed 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.

PubMed: 24374628
DOI: 10.1073/pnas.1321032111

Experimental method

X-RAY DIFFRACTION (2.406 Å)