2NUB image
Deposition Date 2006-11-09
Release Date 2007-02-06
Last Version Date 2023-10-25
Entry Detail
PDB ID:
2NUB
Title:
Structure of Aquifex aeolicus Argonuate
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.20 Å
R-Value Free:
0.31
R-Value Work:
0.23
Space Group:
I 4 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Argonaute
Gene (Uniprot):ago
Chain IDs:A
Chain Length:706
Number of Molecules:1
Biological Source:Aquifex aeolicus
Primary Citation
Structure of Aquifex aeolicus argonaute highlights conformational flexibility of the PAZ domain as a potential regulator of RNA-induced silencing complex function.
J.Biol.Chem. 282 13824 13832 (2007)
PMID: 17130125 DOI: 10.1074/jbc.M608619200

Abstact

Gene silencing mediated by RNA interference requires the sequence-specific recognition of target mRNA by the endonuclease Argonaute, the primary enzymatic component of the RNA-induced silencing complex. We report the crystal structure of Aquifex aeolicus Argonaute, refined at 3.2A resolution. Relative to recent Argonaute structures, a 24 degrees reorientation of the PAZ domain in our structure opens a basic cleft between the N-terminal and PAZ domains, exposing the guide strand binding pocket of PAZ. This rearrangement leads to a branched, Y-shaped system of grooves that extends through the molecule and merges in a central channel containing the catalytic residues. A 5.5-ns molecular dynamics simulation of Argonaute shows a strong tendency of the PAZ and N-terminal domains to be mobile. Binding of single-stranded DNA to Argonaute monitored by total internal reflection fluorescence spectroscopy shows biphasic kinetics, also indicative of domain rearrangement upon DNA binding. Conformational rearrangement of the PAZ domain may therefore be critical for the catalytic cycle of Argonaute and the RNA-induced silencing complex.

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