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

PDB id:

4kpy

Name:

DNA binding protein/DNA

Title:

DNA binding protein and DNA complex structure

Structure:

Uncharacterized protein. Chain: a, b. Engineered: yes. 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'). Chain: c, e. Engineered: yes. DNA (5'-d(p Tp Ap Cp Tp Ap Cp Cp Tp Cp G)-3').

Source:

Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Gene: tt_p0026. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.41Å R-factor: 0.193 R-free: 0.235

Authors:

G.Sheng,H.Zhao,J.Wang,Y.Rao,Y.Wang

Key ref:

G.Sheng et al. (2014). Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc Natl Acad Sci U S A, 111, 652-657. PubMed id: 24374628 DOI: 10.1073/pnas.1321032111

Date:

14-May-13 Release date: 29-Jan-14

Protein chains

Q746M7  (AGO_THET2) -  Protein argonaute from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 685 a.a.

Struc: 676 a.a.

DNA/RNA chains

T-G-A-G-G-T-A-G-T-A-G-G-T-T-G-T 16 bases

T-A-C-T-A-C-C-T-C-G 10 bases

T-G-A-G-G-T-A-G-T-A-G-G-T-T-G-T 16 bases

T-A-C-T-A-C-C-T-C-G 10 bases

A-C-A-A-C-C 6 bases

A-C-A-A-C-C 6 bases

Enzyme reactions

• Enzyme class: E.C.3.1.24.- - ?????

DOI no: 10.1073/pnas.1321032111

Proc Natl Acad Sci U S A 111:652-657 (2014)

PubMed id: 24374628

Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.

G.Sheng, H.Zhao, J.Wang, Y.Rao, W.Tian, D.C.Swarts, J.van der Oost, D.J.Patel, Y.Wang.

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.