PDBsum entry 5guh

Hydrolase/RNA

PDB id: 5guh

Contents

Protein chain

759 a.a.

DNA/RNA

Metals

_MG ×2

Waters ×84

PDB id:

5guh

Name:

Hydrolase/RNA

Title:

Crystal structure of silkworm piwi-clade argonaute siwi bound to pirna

Structure:

Piwi. Chain: a. Synonym: piwi,siwi,uncharacterized protein. Other_details: the n-terminal region (residues 1-129) was truncated by thermolysin treatment.. RNA (28-mer). Chain: b. Other_details: the bound rnas are co-purified endogenous pirnas, which have divergent sequences and lengths.

Source:

Bombyx mori. Silk moth. Organism_taxid: 7091. Organism_taxid: 7091

Resolution:

2.40Å R-factor: 0.211 R-free: 0.236

Authors:

N.Matsumoto,H.Nishimasu,R.Ishitani,O.Nureki

Key ref:

N.Matsumoto et al. (2016). Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA. Cell, 167, 484. PubMed id: 27693359

Date:

29-Aug-16 Release date: 19-Oct-16

Protein chain

A8D8P8  (SIWI_BOMMO) -  Piwi-like protein Siwi from Bombyx mori

Seq: 899 a.a.

Struc: 759 a.a.

DNA/RNA chain

U-A-U-U-U-U-U-OMU 8 bases

Enzyme reactions

• Enzyme class: E.C.3.1.26.- - ?????

Cell 167:484 (2016)

PubMed id: 27693359

Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA.

N.Matsumoto, H.Nishimasu, K.Sakakibara, K.M.Nishida, T.Hirano, R.Ishitani, H.Siomi, M.C.Siomi, O.Nureki.

ABSTRACT

PIWI-clade Argonaute proteins associate with PIWI-interacting RNAs (piRNAs) and silence transposable elements in animal gonads. Here, we report the crystal structure of a silkworm PIWI-clade Argonaute, Siwi, bound to the endogenous piRNA, at 2.4 Å resolution. Siwi adopts a bilobed architecture consisting of N-PAZ and MID-PIWI lobes, in which the 5' and 3' ends of the bound piRNA are anchored by the MID-PIWI and PAZ domains, respectively. A structural comparison of Siwi with AGO-clade Argonautes reveals notable differences in their nucleic-acid-binding channels, likely reflecting the distinct lengths of their guide RNAs and their mechanistic differences in guide RNA loading and cleavage product release. In addition, the structure reveals that Siwi and prokaryotic, but not eukaryotic, AGO-clade Argonautes share unexpected similarities, such as metal-dependent 5'-phosphate recognition and a potential structural transition during the catalytic-tetrad formation. Overall, this study provides a critical starting point toward a mechanistic understanding of piRNA-mediated transposon silencing.